An environmentally friendly extraction strategy based on an MSAT (Medium Scale Ambient Temperature) system was applied to Quercus ilex and Quercus robur acorns with the aim of maximizing polyphenolic yield and antioxidant activity while minimizing solvent consumption. Extracts were evaluated in terms of total polyphenolic content, antioxidant activity, reducing sugars, proteins, targeted polyphenols quantified by UHPLC-QToF, and antimicrobial activity. Optimal extractions from Quercus ilex reached 25,072 mg GAE L−1 and 162 mmol TE L−1, while Quercus robur extracts showed markedly superior values of 35,822 mg GAE L−1 and 234 mmol TE L−1. Polyphenol quantification revealed higher concentrations of gallotannins in Quercus robur and procyanidins and catechin in Quercus ilex. The extracts showed strong antibacterial activity, especially Quercus ilex against S. aureus with a MIC ≤ 0.63%. Furthermore, it has been demonstrated for the first time that acorn extracts can inhibit the growth of Phytophthora cinnamomi in vitro, with Quercus robur extracts having a MIC ≤ 0.1% and Quercus ilex extracts ≤ 1%.